Transcript SAS and Biometry Training Session I Getting your data into SAS

Molecular Genetic Variation in Cogongrass
Near the Point of Initial Introduction into
the Southeastern United States
Ludovic J.A.Capo-chichi
W.H. Faircloth,A.G. Williamson
M. G. Patterson, J.H. Miller
S. L. Noffsinger, and Edzard van Santen
Auburn University
Botanical Characteristics of I. cylindrica
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Inflorescences of I. cylindrica
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Morphological differences
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Infestation with I. cylindrica
Year
Infested (ha)
Location
Reference
1954
200
Mobile Cty
Tabor (1952)
1974
4,000
Mobile Cty
Dickens (1974)
2003
200,000
SW Alabama Faircloth et al. (2003)
 20-fold increase from 1954 to 1974
 50-fold increase from 1974 to 2003
Most likely an underestimate of the total area currently infested
 Survey concentrated on highway right-of-ways
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Sampling Cogongrass in Mobile Cty
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Amplified Fragment Length Polymorphism (AFLP)
A PCR-based molecular technique that can provide
An estimate of genetic diversity in introduced species,
Evidence of multiple introductions,
Evidence of zones of hybridization, and
Identify compatible relationships between biocontrol agent
and weed host
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AFLP protocol
Extract total genomic DNA (CTAB protocol)
Quantify and standardize DNA concentrations
Standard AFLP protocol
Pre-amplification
Selective amplification
Banding patterns visualized with IR dyes
Manual scoring
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Statistical Analysis
Cluster analysis
Relationship based on the banding profile of individuals
Assigns these individuals to artificial clusters
Canonical discriminant analysis
Analysis based on preexisting groups (sampling sites)
Maximizes among group differences based on the common
profile of members of a group
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Statistical Analysis (cont.)
Gene diversity estimates
 A measure of genetic variance of a population equal
to the probability of identity of randomly chosen genes
Gene flow (Nm) estimates
 Refers to all mechanisms resulting in the movement of
genes from one population to another
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Polymorphism and Gene Diversity
Gene
Polymorhic markers
diversity HT
Population
n
%
P1
59
43
0.10
P2
55
40
0.14
P3
68
50
0.16
P4
58
42
0.13
P5
48
35
0.09
P6
59
43
0.10
P7
44
32
0.11
P8
45
33
0.09
Pi
27
20
0.07
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AFLP Fingerprint - Grouping by Location
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Analysis of Molecular Variance (AMOVA)
Source of
Variance
Fixation
variation
df components percentage Index ФST
Among
populations
8
5.8
44
0.44
Within
populations 126
7.5
56
Total
13.3
100
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Canonical Discriminant Analysis
Can3
P1
P5
13.59
P2, P4
P6, P7, P8
2.41
Pi
-8.78
10.44
P3
1.53
-19.97
25.85
-7.39
Can2
6.69
Can1
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-12.47
-31.63
-16.30
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Gene Flow Estimates
R = 0.09
6.0
P2/P3
5.0
Nm
4.0
3.0
P2/P3
2.0
P4/Pi
P8/Pi
Nm > 1
P4/P5
P7/Pi
1.0
Nm < 1
P2/Pi
0.0
0.1
P5/Pi
P3/Pi
0.3
1
P6/Pi
P1/Pi
3
10
30
100
log Distance (km)
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Why are Gene Flow Estimates N.S.
Close geographic proximity
Statistics are not very sensitive
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Summary

AFLPs work well in weedy species
 Populations of I. cylindrica near the point of
initial introduction contain quite a bit of genetic
variation
 74 % of all AFLP markers showed polymorphism
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Summary (cont.)
 Founder effect. The founder source contains
the lowest gene diversity. Something that
was not well-known
56 % of the molecular variance was
contained within populations
 Evidence that populations are
differentiated
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Summary (cont.)
 In both cases (molecular and historical) there is
no evidence for private alleles
 Creation of genetic diversity
 Genetic recombination
 Variation created at vegetative level
Anthropogenic dispersal is one of the powerful
agents for local dispersal of I. cylindrica
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“ Invasive Plants – Arming to Defend and Win”
Southeast Exotic Pest Plant Council’s 7th Annual Conference
Alabama Invasive Plant Council’s 3rd Annual Conference
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